6215a31ba6da621d6de9254f33ebb084 *DESCRIPTION
07c88692ce88af0dd308506193834202 *LICENSE
2ff16a70b62af9b57758e00a0961c476 *NAMESPACE
3b1eab7759335ab114e2a84ec0382b81 *NEWS
e1d7b9d49ace2d7bff3ceb4021dd0250 *R/RcppExports.R
998e55a45f8436a021cebca098c95cd4 *R/abc_calibration.R
b7c2f45249dc3e4d030d29e210db021c *R/allocation_diagnostics.R
13a0fec35e3d3f300fad1fff9062b9e2 *R/check_required_columns.R
990d86674c09abe75a3d0c04dab080e3 *R/classification_sensitivity.R
34d9c5573894a46200b9995d8fae1705 *R/classify_hicpotts.R
de40e8f5eee54bb1374759f3f48934a9 *R/combine_blocks.R
9446c873aff243f4b8290e2ccc868246 *R/compute_probabilities.R
1d389610d1816909a1cd1dfa2b9716d6 *R/dataset_fingerprint.R
6c126e65a59aa6c2e9d61e01d904ffdc *R/engineering.R
cda5b5f71da65a0803fd491f594649ab *R/genomic_distance.R
cad2b320ed0f2859d76d87527c24f6e0 *R/globals.R
a6187591465678def0825c4357ad2031 *R/hicpotts_diagnostics_and_summaries.R
cbac5c954f62a4081ee36501be7fe6ef *R/hicpotts_inference_improvements.R
1694fad13680b9497faecbee2350bd1d *R/hicpotts_mode_consensus.R
dbd8cb6eae3960186964c6c1321538e1 *R/hicpotts_robust_estimation.R
677d41509a3535c4c9d103f53aef3dcd *R/likelihood.R
7225ac36a36c5bdf4afd250d95f96f4b *R/likelihood_potts.R
ea298bbf9e5a5b4ebec37d1165efa0a9 *R/mirror_half_matrix.R
a695ed8b40e055b0e2a5274d071e7108 *R/plot_matrix.R
68197eee8c5a825f004f0a3d6f483d38 *R/posterior.R
c07c8e18cc98e1a2f9d66130950b1514 *R/posterior_density.R
d7423b0b6665f2982d80f65d139c6dc3 *R/prepare_data.R
fcb4b850927bb2c3b5bb53f2c91a677e *R/prior_modelling.R
cb52f562068556dd7e7a6bb8d6ac5625 *R/prior_modelling_size_NB_ZINB.R
2b7b82cd00b4d6e951bf44b602db1fd9 *R/prior_potts.R
33bdafb9a5a43c9daed16a62c2a8b73f *R/process_data.R
23c1be9fdd75bc4b8a99b03df8096445 *R/relabel_hicpotts.R
46ed7016d9d3258c48f48fa29bb9addd *R/run_chain_unified.R
0667ab9bc9ac5fa6a7ab999c5e87b91b *R/sensitivity_workflow.R
5c0d55eb00c7c543d04832dbcc70189a *R/simulate_potts_truth.R
5eb61f4ae9403c7f7a033d2314860dc9 *R/sources_of_biases_model.R
6517d5608a897d128ff8121ce4ad1ce7 *R/validate_counts.R
8b20ed64025031a54ae8d5fc710db477 *R/validate_simulation.R
72548038045076b65ebf46e97ff8b63b *R/zzz.R
2c315190f8f47162dc08fa434e7ce16c *README.md
c62a48eeb063b7ec9275de632db6b13f *build/vignette.rds
9f8ca91595ab2bc3a0032ac654b11593 *inst/doc/HiCPotts_function_reference.R
7ff2ea8445da6d7a058d0bbfe623d7de *inst/doc/HiCPotts_function_reference.Rmd
220a842743579b09c715f90e9f9d514d *inst/doc/HiCPotts_function_reference.html
591c3c2f11b9d87bb7efeb36416f74cd *inst/doc/HiCPotts_vignette.R
875419d9e5cc668674b3a451c9688853 *inst/doc/HiCPotts_vignette.Rmd
d30ff92e87142524bfa29cd013052294 *inst/doc/HiCPotts_vignette.html
b14d49a78d1b5cb053564e4014d882ef *inst/extdata/BG3_WT_merged_hic_matrix_chr4_100Kb.cool
57c32a850bd959b46b4f83d03962d138 *inst/extdata/DNaseI_BG3_gr_chr4.bedGraph
0bd3f20c51ff156b1ba70c24af4ad403 *inst/extdata/dm3ToDm6_chr4_only.chain
c3364acd3f1d21dfaf89bb58e81b5725 *inst/extdata/dm6_TEs_chr4.gtf
e408855fd9d9c7a0c1ee6d84516d2c71 *inst/extdata/test_data2.csv
1b85cc85f991d2bb2aa61dad1ee1012d *inst/scripts
07435b683006a5a13053425d9f88d735 *man/HiCPotts-package.Rd
eb4bc698cd74f898e894925e3ca7a505 *man/allocation_diagnostics.Rd
ac1fbc0bf8b6c123fbf2a1da6497e819 *man/classify_hicpotts.Rd
166ea3f3e6d2c6627aae2695ee56685c *man/combine_hicpotts_blocks.Rd
853b9f842a6332ae5db8b8bad23182a4 *man/compute_HMRFHiC_probabilities.Rd
5cb82ff7341972a3f77e8cf14aac457b *man/diagnose_hicpotts_fit.Rd
118817e20cb197b102aefcf1375e4fd4 *man/get_data.Rd
269edd5358643bc2f78b872f000815e2 *man/plot_hicpotts_mcmc_by_component.Rd
cf8c306ff5a3ff56c867c0fc803174ff *man/plot_upper_prob_lower_count.Rd
413c495739bc2deb2eafad20fa93efd2 *man/posterior_predictive_hicpotts.Rd
2c865ebdfcfd26f2795959e109eeba4f *man/process_data.Rd
6eb6489b1f4f20db644b9f26dce091e4 *man/relabel_hicpotts.Rd
86541ca5d4fec8a53a216ccbfdc9789a *man/run_chain_betas.Rd
f6b689c279b35e368fa5f3eed8c925fc *man/summarise_hicpotts_parameters.Rd
f5f947262980449d5e0b397e934ee3f9 *man/summarise_hicpotts_probabilities.Rd
98d74bb2daff032040a428b4a5a38f8c *src/MCMC_chain.cpp
8043e3747926cbc6e1427ff1fb80faf3 *src/Makevars
11af6753d29cf1ed3e0541eeae6ae88d *src/Neighbours_function.cpp
56e1f45fd468d7d8e30b6975242c0289 *src/RcppExports.cpp
8fe39193743738eae5a8b21bb026d16e *src/abc_s1s2_gamma.h
d6e2037b20807bbcfcead40068616d44 *src/hicpotts_pair_weight.h
5fb406ef312bcff0eb46c1260dca082d *src/potts_posterior.cpp
34acb29ea8e2d5737c8938922e5f31e0 *tests/testthat.R
b05d555bf7eaa8b9c085976846fca79e *tests/testthat/test-RcppExports.R
4632469ac165ec8b0e3b086408988f97 *tests/testthat/test-abc-augmented-state.R
ebb01275c609d6db33ad537bcef815fc *tests/testthat/test-abc-gamma.R
b60ce8cd394ecfad0227572c5e4f6c30 *tests/testthat/test-allocation-diagnostics.R
58e39ad7cadab63c0f97077c9ecf1810 *tests/testthat/test-audit-fixes-2.R
0c088fbcecb09de447facedd8140c481 *tests/testthat/test-audit-fixes.R
b8139ec76b94d2da3bf5554f82dbd9ec *tests/testthat/test-branch-gamma-mixing.R
0bb44fd024dea7f51332ebfc81dcb3d0 *tests/testthat/test-classify-hicpotts.R
67d46b6af9ae6138adf9a5527c29128b *tests/testthat/test-cluster-detailed-balance.R
97eb90b782dcfbe33061520a0f0aac03 *tests/testthat/test-combine-blocks.R
bb6e1e3135eb7251eb27148b6fced748 *tests/testthat/test-compute_probabilities.R
9b8b13d50bd2640fbe758590b12ebf7d *tests/testthat/test-dataset-fingerprint.R
0f851b8abffa7e17ff10adf021acc96c *tests/testthat/test-engineering-safeguards.R
a9c53afb9cd31089194f3c8a5fafec73 *tests/testthat/test-genomic-distance.R
7cb1a27a4e67f13638a66b0816090f6b *tests/testthat/test-inference-improvements.R
04b96266d19a4e23bd407a0faf9b48d4 *tests/testthat/test-likelihood.R
f1315cf5bdff547da454078dd65189c5 *tests/testthat/test-likelihood_potts.R
cb428a38858786abd2bfc71c8f2e7df9 *tests/testthat/test-mirror-half-matrix.R
c7cc2b8089124a70039c26aa6cba37c6 *tests/testthat/test-mode-consensus-soft.R
a61cbf6522a65e426611b0d45ffbc896 *tests/testthat/test-mode-consensus.R
16fdcde72e950721bcb2f1d345618931 *tests/testthat/test-neighbours.R
0e496e6cb0b2d42627847568a5bb41de *tests/testthat/test-noise-relationship.R
a86d5df0839d39c275f7697c1ddb523c *tests/testthat/test-plot-matrix.R
72e810aeffc23fced326a7110ba7e6e0 *tests/testthat/test-pool-block-parameters.R
149f624798b9f763e6827269f2bcc0ed *tests/testthat/test-posterior.R
bca877f2c076f5020a6fc91a92ea5355 *tests/testthat/test-posterior_density.R
618c6804cb593e2b19270b3aedd1ba0d *tests/testthat/test-prepare_data.R
deb90f8fd2aa38615ccef9890d604857 *tests/testthat/test-prior_modelling.R
b13e8230bc1c5daf427d110a92ac7d66 *tests/testthat/test-prior_modelling_size_NB_ZINB.R
e74ada931cae8ff246d55c1e76df6211 *tests/testthat/test-prior_potts.R
e4437a607416d730164d03ad3f981cdb *tests/testthat/test-process_data.R
3b3c92fa07a42e1c45e9f5a500b39666 *tests/testthat/test-public-interface-consolidation.R
da4680ef0c5c436d94e4d5d1f75b3c1b *tests/testthat/test-pz_123.R
95a4efc7f7caa5c6948fe068ca4e01a0 *tests/testthat/test-rank-normalized-diagnostics.R
66e33e34bc433488058610978df4ac89 *tests/testthat/test-release-safeguards.R
929d3911ab467aa65fc3082c28e6d84c *tests/testthat/test-run_chain.R
377a3a8edf330815b80a88b5e0367cdf *tests/testthat/test-sensitivity-validation.R
97569662b74811920c2f1153e58133db *tests/testthat/test-sources_of_biases_model.R
07b6a8a74882c05fcca2596960ddf9f0 *tests/testthat/test-theta-detailed-balance.R
7ff2ea8445da6d7a058d0bbfe623d7de *vignettes/HiCPotts_function_reference.Rmd
875419d9e5cc668674b3a451c9688853 *vignettes/HiCPotts_vignette.Rmd
